def test_video2stim():
reload(image)
reload(video)
# Smoke-test example video
from skvideo import datasets
implant = implants.ArgusI()
video.video2stim(datasets.bikes(), implant)
with pytest.raises(OSError):
video.video2stim('no-such-file.avi', implant)
def test_video2pulsetrain():
reload(stimuli)
implant = implants.ArgusI()
with pytest.raises(OSError):
stimuli.video2pulsetrain('no-such-file.avi', implant)
# Smoke-test example video
from skvideo import datasets
stimuli.video2pulsetrain(datasets.bikes(), implant)
def test_parse_pulse_trains():
# Specify pulse trains in a number of different ways and make sure they
# are all identical after parsing
# Create some p2p.implants
argus = implants.ArgusI()
simple = implants.ElectrodeArray('subretinal', 0, 0, 0, 0)
pt_zero = utils.TimeSeries(1, np.zeros(1000))
pt_nonzero = utils.TimeSeries(1, np.random.rand(1000))
# Test 1
# ------
# Specify wrong number of pulse trains
with pytest.raises(ValueError):
stimuli.parse_pulse_trains(pt_nonzero, argus)
with pytest.raises(ValueError):
stimuli.parse_pulse_trains([pt_nonzero], argus)
with pytest.raises(ValueError):
stimuli.parse_pulse_trains([pt_nonzero] *
(argus.num_electrodes - 1),
argus)
with pytest.raises(ValueError):
stimuli.parse_pulse_trains([pt_nonzero] * 2, simple)
# Test 2
# ------
# Send non-zero pulse train to specific electrode
el_name = 'B3'
el_idx = argus.get_index(el_name)
# Specify a list of 16 pulse trains (one for each electrode)
pt0_in = [pt_zero] * argus.num_electrodes
pt0_in[el_idx] = pt_nonzero
pt0_out = stimuli.parse_pulse_trains(pt0_in, argus)
# Specify a dict with non-zero pulse trains
pt1_in = {el_name: pt_nonzero}
pt1_out = stimuli.parse_pulse_trains(pt1_in, argus)
# Make sure the two give the same result
for p0, p1 in zip(pt0_out, pt1_out):
npt.assert_equal(p0.data, p1.data)
# Test 3
# ------
# Smoke testing
stimuli.parse_pulse_trains([pt_zero] * argus.num_electrodes, argus)
stimuli.parse_pulse_trains(pt_zero, simple)
stimuli.parse_pulse_trains([pt_zero], simple)
def test_ScoreboardModel():
# ScoreboardModel automatically sets `rho`:
model = models.ScoreboardModel(engine='serial', xystep=5)
npt.assert_equal(hasattr(model, 'rho'), True)
# User can set `rho`:
model.rho = 123
npt.assert_equal(model.rho, 123)
model.build(rho=987)
npt.assert_equal(model.rho, 987)
# Zero in = zero out:
implant = implants.ArgusI(stim=np.zeros(16))
npt.assert_almost_equal(model.predict_percept(implant), 0)
def test_image2pulsetrain():
# Range of values
amp_min = 2
amp_max = 15
# Create a standard Argus I array
implant = implants.ArgusI()
# Create a small image with 1 pixel per electrode
img = np.zeros((4, 4))
# An all-zero image should give us a really boring stimulation protocol
pulses = stimuli.image2pulsetrain(img, implant, valrange=[amp_min,
amp_max])
for pt in pulses:
npt.assert_equal(pt.data.max(), amp_min)
# Now put some structure in the image
img[1, 1] = img[1, 2] = img[2, 1] = img[2, 2] = 0.75
expected_max = [amp_max, 0.75 * (amp_max - amp_min) + amp_min]
for max_contrast, val_max in zip([True, False], expected_max):
pt = stimuli.image2pulsetrain(img, implant, coding='amplitude',
max_contrast=max_contrast,
valrange=[amp_min, amp_max])
# Make sure we have one pulse train per electrode
npt.assert_equal(len(pt), implant.num_electrodes)
# Make sure the brightest electrode has `amp_max`
npt.assert_almost_equal(np.max([p.data.max() for p in pt]),
val_max)
# Make sure the dimmest electrode has `amp_min` as max amplitude
npt.assert_almost_equal(np.min([np.abs(p.data).max() for p in pt]),
amp_min)
# Invalid implant
with pytest.raises(TypeError):
stimuli.image2pulsetrain("rainbow_cat.jpg", np.zeros(10))
with pytest.raises(TypeError):
e_array = implants.ElectrodeArray('epiretinal', 100, 0, 0)
stimuli.image2pulsetrain("rainbow_cat.jpg", e_array)
# Invalid image
with pytest.raises(IOError):
stimuli.image2pulsetrain("rainbow_cat.jpg", implants.ArgusI())
# Smoke-test RGB
stimuli.image2pulsetrain(np.zeros((10, 10, 3)), implants.ArgusI())
# Smoke-test invert
stimuli.image2pulsetrain(np.zeros((10, 10, 3)), implants.ArgusI(),
invert=True)
# Smoke-test normalize
stimuli.image2pulsetrain(np.ones((10, 10, 3)) * 2,
implants.ArgusI(), invert=True)
# Smoke-test frequency coding
stimuli.image2pulsetrain(np.zeros((10, 10, 3)), implants.ArgusI(),
coding='frequency')
# Invalid coding
with pytest.raises(ValueError):
stimuli.image2pulsetrain(np.zeros((10, 10)), implants.ArgusI(),
coding='n/a')
# Trigger an import error
with mock.patch.dict("sys.modules", {"skimage": {}, "skimage.io": {}}):
with pytest.raises(ImportError):
reload(stimuli)
stimuli.image2pulsetrain(img, implant)
def test_ArgusI(ztype, x, y, rot):
# Create an ArgusI and make sure location is correct
# Height `z` can either be a float or a list
z = 100 if ztype == 'float' else np.ones(16) * 20
argus = implants.ArgusI(x, y, z=z, rot=rot)
# Slots:
npt.assert_equal(hasattr(argus, '__slots__'), True)
npt.assert_equal(hasattr(argus, '__dict__'), False)
# Coordinates of first electrode
xy = np.array([-1200, -1200]).T
# Rotate
rot_rad = np.deg2rad(rot)
R = np.array(
[np.cos(rot_rad), -np.sin(rot_rad),
np.sin(rot_rad),
np.cos(rot_rad)]).reshape((2, 2))
xy = np.matmul(R, xy)
# Then off-set: Make sure first electrode is placed
# correctly
npt.assert_almost_equal(argus['A1'].x, xy[0] + x)
npt.assert_almost_equal(argus['A1'].y, xy[1] + y)
# Make sure array center is still (x,y)
y_center = argus['D1'].y + (argus['A4'].y - argus['D1'].y) / 2
npt.assert_almost_equal(y_center, y)
x_center = argus['A1'].x + (argus['D4'].x - argus['A1'].x) / 2
npt.assert_almost_equal(x_center, x)
# Check radii of electrodes
for e in ['A1', 'A3', 'B2', 'C1', 'D4']:
npt.assert_almost_equal(argus[e].r, 125)
for e in ['A2', 'A4', 'B1', 'C2', 'D3']:
npt.assert_almost_equal(argus[e].r, 250)
# Check location of the tack
tack = np.matmul(R, [-2000, 0])
tack = tuple(tack + [x_center, y_center])
# `h` must have the right dimensions
with pytest.raises(ValueError):
implants.ArgusI(x=-100, y=10, z=np.zeros(5))
with pytest.raises(ValueError):
implants.ArgusI(x=-100, y=10, z=[1, 2, 3])
# Indexing must work for both integers and electrode names
for use_legacy_names in [True, False]:
argus = implants.ArgusI(use_legacy_names=use_legacy_names)
for idx, (name, electrode) in enumerate(argus.electrodes.items()):
npt.assert_equal(electrode, argus[idx])
npt.assert_equal(electrode, argus[name])
npt.assert_equal(argus["unlikely name for an electrode"], None)
# Right-eye implant:
xc, yc = 500, -500
argus_re = implants.ArgusI(eye='RE', x=xc, y=yc)
npt.assert_equal(argus_re['D1'].x > argus_re['A1'].x, True)
npt.assert_almost_equal(argus_re['D1'].y, argus_re['A1'].y)
# need to adjust for reflection about y-axis
# Left-eye implant:
argus_le = implants.ArgusI(eye='LE', x=xc, y=yc)
npt.assert_equal(argus_le['A1'].x > argus_le['D4'].x, True)
npt.assert_almost_equal(argus_le['D1'].y, argus_le['A1'].y)
# In both left and right eyes, rotation with positive angle should be
# counter-clock-wise (CCW): for (x>0,y>0), decreasing x and increasing y
for eye, el in zip(['LE', 'RE'], ['A1', 'D1']):
before = implants.ArgusI(eye=eye)
after = implants.ArgusI(eye=eye, rot=10)
npt.assert_equal(after[el].x > before[el].x, True)
npt.assert_equal(after[el].y > before[el].y, True)
# Check naming scheme
argus = implants.ArgusI(use_legacy_names=False)
npt.assert_equal(argus.electrode_names[15], 'D4')
npt.assert_equal(argus.electrode_names[0], 'A1')
argus = implants.ArgusI(use_legacy_names=True)
npt.assert_equal(argus.electrode_names[15], 'M1')
npt.assert_equal(argus.electrode_names[0], 'L6')
# Set a stimulus via dict:
argus = implants.ArgusI(stim={'B3': 13})
npt.assert_equal(argus.stim.shape, (1, 1))
npt.assert_equal(argus.stim.electrodes, ['B3'])
# Set a stimulus via array:
argus = implants.ArgusI(stim=np.ones(16))
npt.assert_equal(argus.stim.shape, (16, 1))
npt.assert_almost_equal(argus.stim.data, 1)